Pacifica Casull is the most feared and hated person by the followers of the God Mauser. Known as the Scrapped Princess, she is the poison that will destroy the world. To avoid being killed by the zealots of Mauser, Pacifica and her adoptive brother and sister leave the village of Manhurin. Her brother, Shannon, is an expert with the sword while Racquel is proficient with magic. At every step of the way, however, someone is constantly trying to kill Pacifica, hoping to somehow avert the catastrophe that is supposed to befall the world on her 16th birthday.
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Pacifica, Shannon and Racquel meet Christopher Armalite for the first time. Raquel Casull saves Pacifica from a Mauser priest. In a quiet moment, Pacifica tells Shannon that she loves him and he tells her that he knows.
Leopold Scorpse is introduced as the party goes with him to meet Sir Barrett, from whom Leopold wants to learn chivalry. Pacifica empowers a dragoon, which she thinks is a lake spirit, to sleep by telling her everything is OK.
The group stays at Winia Chester's inn. They are low on money so Racquel and Pacifica go to work selling Soopy-kun bread. Meanwhile, Chris kidnaps Winia, planning to use her as bait to lure the Cassulls. This begins Chris and Winia's special relationship.
Shannon defeats Chris and saves Winia. Chris then helps them by recalling his knights under pretext. A Mauser operative creates a monster that threatens the city, causing Pacifica's powers to manifest themselves when she destroys it.
The group encounters Kidaf Gillot the Silencer who can control electronic bugs. A bug poisons Pacifica, and Leo and Racquel go to Sir Barrett for aid. They confront the minstrel and his bugs at the bug's lair, defeating them and obtaining a curative plant.
Pacifica recovers from her illness but Galil kidnaps Racquel and Shannon. Leo and Pacifica are given their location by Kidaf Gillot and go to save them. Ultimately, Zeferis makes Shannon a D Knight and helps him destroy Galil.
Chris questions the Mauser high priest about the validity of the 5111th prophecy. Shannon befriends Sim, a little girl, and brings her home with him. At the end, Zeferis gives Pacifica a dagger and asks her to kill Sim.
Zeferis explains that Sim is really Cz, a Peacemaker, and an enemy of the group. Pacifica refuses to kill her, and Sim runs off. Pacifica goes after her, and finds her with Steyr. Steyr changes Sim into Cz, but Shannon and Zeferis force them to retreat.
The group meets a Mauser priest at a restaurant and travels with him. They discover a hidden village of Browning heretics who imprison Bergens. The leaders of the village, Lenard and Elfetine, ask them to watch as they correct the world in a ceremony.
Lenard has brainwashed Elfitine into helping him destroy the village as a tribute to Mauser. The group helps foil his plan and continue on towards Giat. Chris goes to visit Pacifica's mother, the queen.
Chris tells Pacifica's mother about Pacifica. Leo and Winia set off to look for Pacifica. The group arrives at Giat and is immediately captured by Seness Giat, the "Beast Princess." At first she appears to be an enemy, but she isn't.
Natalie explain that Pacifica is the "Providence Breaker" and that Guardians, people with magic powers, have been created to protect her. She is the only human capable of resisting the Peacemakers. Shannon and Zeferis combine and drive off Steyr.
Eirote explains that humans are trapped in their world because of a battle with aliens. The group wants to go to Leinwan because the Peacemakers are threatening civilians, but the dragoons stop their transportation, a mobile fortress.
Natalie brainwashes Shannon in order to stop the group from going to Leinwan, but Pacifica reverses it and they continue on. Meanwhile, the Leinwan King is readying his most powerful weapons to stop them.
Winia visits Chris, but he goes past her without a word, giving her a strange look. The Leinwen priests fire their most powerful magic and damage the ship as the Peacemakers restrict its defenses.
The blast from the battle gives Pacifica amnesia and she meets and moves in with Fulle. Leo, Winia, Racquel and others find her in the city, but let her stay at Fulle's. Cz decides to tail Shannon as he looks for his sisters.
Pacifica continues to enjoy her life with Fulle, while the military is close to catching her. Cz, more passionate than a typical Peacemaker, explains to Shannon why the status quo should be left alone.
Pacifica, Fulle, Leo and Winia disguise themselves and escape the city. Leo and his rival for Pacifica's love, Fulle, go back for horses. Fulle is killed making sure that Leo can escape. Shannon and Cz grow closer together.
Pacifica is captured by Chris and his unit. She is placed in a dungeon cell next to her mother. Without realizing she's talking about herself, she tells her mother of her life. After seeing her daughter for the first time in 15 years, Pacifica's mother dies.
The Leinwen military commander tries to use Pacifica as a bargaining chip with Steyr and the Peacemakers. This triggers a world reset where the Peacemakers are allowed to kill 90% of the human race, and Steyr and Socom start to demolish the city. Also, Pacifica regains her memory after Shannon jumps in to save her when the soldiers try to kill her.
Shannon and Senesss kill Steyr, forcing Cz and Socom to retreat. Then, Chris and his unit save Pacifica. Again, Pacifica thinks that everyone would be better off if she died, but Shannon challenges her thinking and she decides she wants to live.
The group, along with Chris's unit, camps in the woods. Celia appears and asks Pacifica if a caged bird (humans) wants to fly in the sky. Cz shows second thoughts about killing Pacifica.
Prince Forsis requests to meet with Pacifica before her 16th birthday. When they meet, he stabs her, and then himself. They are then attacked by the military, and Shannon goes to fight Socom.
Pacifica dies. After Pacifica dies, she is called into Celia's world. Celia asks her advice, freeing the world from its cage. Pacifica's life is restored, and the three siblings go back to their village. Leo proposes again, and Pacifica turns him down.